To create an acknowledgement letter for your donations, for Step 1 you must choose Transactions for your filter audience. On Step 2 the Purpose needs to be set to Acknowledgment. 

In Bloomerang, only the Purpose of “Acknowledgement” will flip the Acknowledged? flag to Yes and the interactions for the letters will be linked to the transactions being acknowledged.

Letters with a purpose of "Receipt" do not affect the Acknowledgement flag on a transaction.